Format of the protocol file

General format

  1. Columns
  2. Rows

Using paired-end reads

Using biological replicates

The protocol file is an important part of every HyLiTE analysis. It allows the user to define:

For specific examples, please refer to the HyLiTE manual

General format

1. Columns

The columns of the protocol file are separated by tabs. They are, from left to right:

  • organism name
  • organism ploidy (an integer value)
  • sample name
  • data: RNAseq or gDNA
  • .fastq file containing the reads

Note

  • The protocol file contains no header line
  • The file names must include their complete paths
  • The data type is relevant for the computation of expression data
  • Using the option -S one can provide alignment files (.sam) instead of read files

2. Rows

Each line represents a single file, even in the case of paired-end reads or biological replicates.

Note

  • The child must be the first organism listed
  • The lines must be grouped by organism, then by sample

Using paired-end reads

For paired-end reads, the reads should be contained in two files. This is represented in the protocol file by two consecutive lines, with the same organism name and the same sample name, but with a different file name.

Using biological replicates

If you have several biological replicates for one or more organisms, just use the same organism name, but a different sample name. Using several biological replicates is particularly helpful as it increases the SNP detection sensitivity while HyLiTE still keeps track of the expression of every replicate individually.